MolNFT v1 · #137930 · protein
Cryoem structure of rhinovirus B14 in complex with C5 Fab (33 degrees celsius, molar ratio 1:1, full particle)
5W3M · C5 antibody variable heavy domain: “Cryoem structure of rhinovirus B14 in complex with C5 Fab (33 degrees celsius, molar ratio 1:1, full particle)”. Electron microscopy, 10 pockets (best druggability 0.76). MolNFT v1 #137930 on…
- PDB
- 5W3M
- Type
- protein
- Length
- 1,024 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C5 antibody variable heavy domain; C5 antibody variable light domain; Viral protein 1…
- UniProt
- P03303
- Pockets
- 10 · best druggability 0.76
Structure
electron microscopy · 6 distinct chains · 9% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | C5 antibody variable heavy domain | protein | 116 | 3% helix, 49% strand | — |
| G | C5 antibody variable light domain | protein | 107 | 3% helix, 50% strand | — |
| A | Viral protein 1 | protein | 273 | 10% helix, 32% strand | P03303 |
| B | Viral protein 3 | protein | 236 | 9% helix, 32% strand | P03303 |
| C | Viral protein 2 | protein | 255 | 14% helix, 36% strand | P03303 |
| D | Viral protein 4 | protein | 37 | 19% helix, 3% strand | P03303 |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.76 | 0.84 | 70 | empty |
| 2 | 118 | 0.76 | 0.95 | 26 | empty |
| 3 | 214 | 0.53 | 0.77 | 33 | empty |
| 4 | 129 | 0.45 | 0.77 | 30 | empty |
| 5 | 110 | 0.41 | 0.76 | 24 | empty |
Interfaces
12 interfaces between chains.
- A–B · 4179 Ų buried · 71 hydrogen bonds · protein-protein
- A–C · 2112 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 1700 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 968 Ų buried · 16 hydrogen bonds · protein-protein
- E–G · 857 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5W3M · CryoEM structure of rhinovirus B14 in complex with C5 Fab (33 degrees Celsius, molar… · the same entry in another collection · chain E against E, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P03303
- Elsewhere: RCSB PDB 5W3M · PDBe 5W3M · UniProt P03303
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